Comparative genomics of Staphylococcus aureus isolates from Africa using virulence and drug resistance markers

Abstract

Introduction There is wide diversity among Staphylococcus aureus lineages colonizing and infecting the African population, yet information on S. aureus infections in Africa is limited. Africa bears a particularly high burden of S. aureus infections in humans. With the globalization trend, there is a need to characterize these infections using resistance and virulence markers to determine whether these markers are shared or specific to particular African countries and/or regions. Due to the enormous increase in international travel and Africa’s porous borders, opportunities for the transmission of resistant microorganisms from one geographic location to another have increased. As a result, both local and regional resistant strains have become vital when designing interventions to contain and combat antimicrobial resistance. Aim: In this study, we characterized the strains of Staphylococcus aureus infecting individuals in different African countries using in silico methods Methodology: We utilized whole-genome sequences of S.aureus isolates from individuals in African countries from the Sequence Read Archive database in the National Centre for Biotechnology Information (NCBI) using a systematic search by Bioproject. The sequences were downloaded, subjected to quality control and genomic analysis was done using Nullarbor pipeline. Results: A total of 29 resistance genes were detected among the sequences with the most prevalent genes being Tet(38), blal-of-Z, blaR1,dfrG, and blaZ found in more than half of the sequences. The least expressed resistance genes included ant(9)-la, aph(2”)-lh, blaR1-2, catA7, catA8, dfrC, fusC, mecR1, mecl-of-mecA, tet(M) and vga(A). A total of 81 virulence genes were expressed among the African population in this study. These genes encode various virulence factors: the capsular polysaccharide (cap8 A through to cap8P), enterotoxins (SEs; sea, seb, sec, sed, seh, sell, selq, and selk), exfoliative toxins (eta, and etb), toxic shock syndrome toxin-1(tst), Panton-Valentine leucocidin cytotoxin (lukS-PV and lukF-PV), staphylococcal complement inhibitor (scn), adhesion factors (fnbA, fnbB, cna, sdrC, sdrD, sdrE, icaA icaB,icaC, icaD, icaR, clfA,and clfB), hemolysins (hly/hla, hlb, hld, hlgA, hlgB, hlgC, hysA), and the type VII secretion system (esaB, essA, essB, essC, esxB, esaC, esxA, and esaC). The most prevalent virulence genes were esaB, cap8N and cap8M which were found in all the 373 sequences and the least prevalent virulence genes were sed(0.8%), eta(3.5%) and etb(1.1%) which were found in less than 20 sequences. Conclusions: We comprehensively conducted molecular characterization of S.aureus using drug resistance and virulence markers in Africa. There is a high rate of tetracycline resistance markers indicating widespread and prolonged misuse of tetracycline in the various African countries.